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327 results • Page 1 of 7
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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 7 days ago by 40k • written 7 days ago by 156k
0
votes
1
reply
163
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 days ago by 76k • written 8 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 15 days ago by 134k • written 3.4 years ago by 76k
0
votes
0
replies
211
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
27 days ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
208
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
4 weeks ago by Ming Tommy Tang ★ 3.4k
13
votes
3
replies
10k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 4 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
4
votes
2
replies
423
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 5 weeks ago by 40k • written 5 weeks ago by ★ 2.3k
0
votes
0
replies
181
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
5 weeks ago by Ming Tommy Tang ★ 3.4k
8
votes
4
replies
3.9k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
6 weeks ago by Hamid Ghaedi 3.0k
6
votes
0
replies
211
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
5 weeks ago by barslmn ★ 1.8k
0
votes
0
replies
217
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
6 weeks ago by Starlitnightly • 0
1
vote
0
replies
278
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 7 weeks ago by 40k • written 7 weeks ago by ★ 3.4k
3
votes
1
reply
300
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 7 weeks ago by 40k • written 7 weeks ago by 8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 weeks ago by • 0 • written 7.5 years ago by 20k
1
vote
0
replies
301
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 weeks ago by 40k • written 9 weeks ago by ★ 3.4k
0
votes
0
replies
409
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
9 weeks ago by Starlitnightly • 0
18
votes
13
replies
6.6k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 9 weeks ago by 53k • written 14 months ago by 76k
2
votes
0
replies
2.7k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 9 weeks ago by 40k • written 9 weeks ago by ★ 3.4k
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 weeks ago by 76k • written 3.5 years ago by 5.5k
3
votes
2
replies
457
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 weeks ago by Ming Tommy Tang ★ 3.4k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 10 weeks ago by • 0 • written 5.2 years ago by ▴ 580
2
votes
0
replies
224
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
4
votes
0
replies
344
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
12 weeks ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
270
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
0
votes
0
replies
287
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
12 weeks ago by sinha.shriprakash ▴ 20
1
vote
2
replies
462
views
Tutorial: How to ask computational biology questions
computational-biology
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
1
vote
0
replies
334
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
2
votes
0
replies
318
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
3 months ago by Ming Tommy Tang ★ 3.4k
1
vote
0
replies
339
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
3 months ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
380
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
3 months ago by Coremine Medical ▴ 10
1
vote
0
replies
357
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 3 months ago by 40k • written 3 months ago by ▴ 10
3
votes
0
replies
645
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
4 months ago by Ming Tommy Tang ★ 3.4k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 months ago by 134k • written 9.8 years ago by 20k
2
votes
0
replies
720
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 6 months ago by 76k • written 6 months ago by ▴ 40
1
vote
0
replies
458
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
6 months ago by Milad ▴ 10
3
votes
2
replies
2.4k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 4 months ago by 40k • written 6.4 years ago by ▴ 100
7
votes
3
replies
1.7k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 5 months ago by ▴ 110 • written 13 months ago by 86k
3
votes
3
replies
2.2k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 7 months ago by 40k • written 17 months ago by ★ 3.3k
1
vote
0
replies
721
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
7 months ago by firestar ★ 1.6k
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
5 months ago by barslmn ★ 1.8k
2
votes
1
reply
1.5k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 8 months ago by 156k • written 8 months ago by ★ 1.8k
3
votes
2
replies
1.5k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
9 weeks ago by Dr.Animo ▴ 60
2
votes
0
replies
837
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 3 months ago by 40k • written 8 months ago by ▴ 350
1
vote
0
replies
2.1k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 3 months ago by 40k • written 8 months ago by ▴ 350
4
votes
0
replies
935
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 3 months ago by 40k • written 8 months ago by ▴ 350
6
votes
0
replies
2.4k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
6 months ago by Novogene ▴ 350
50
votes
1
reply
7.4k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 7 months ago by 40k • written 3.0 years ago by 76k
1
vote
3
replies
680
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
5 months ago by barslmn ★ 1.8k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.0 years ago by 86k
13
votes
31
replies
5.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
327 results • Page 1 of 7
Recent Votes
What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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Popular Question to zx8754 11k
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Recent Replies
Answer: Importance of Data Structures for Bioinformatics? by xiaoguang ▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings by xiaoguang ▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files? by xiaoguang ▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data by Diana • 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings by d-cameron ★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data? by luffy ▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq by Chris ▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics? by d-cameron ★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu by dk0319 ▴ 70
Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
Comment: manhattan plot with vcf information by sooni ▴ 10
I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
Comment: Importance of Data Structures for Bioinformatics? by dsull ★ 4.6k
If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
Comment: How to DESeq2 using miRNA data obtained using TCGAbiolinks by swbarnes2 13k
miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to ge…
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
Hi Amy, I understand, this is why I said, > "The degree to which this is possible depends on the relative content > of each study - e.g. …
Answer: What is the difference between norm --multiallelics -any versus --atomize? by Ram 40k
I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
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